the phylogeographic challenge to creationism

Sorry -- didn't mean to submit this. (My wife took over the computer and submitted it for me before I was satisfied with it -- since I was about to leave home for the day.)This message has been edited by TimChase, 12-09-2005 11:26 AM

You are right, of course. I shouldn't have stated this as if they had actually proven that the mechanism was hypermutation. I don't if I was just being in a hurry, sloppy or misremembering. My apologies.Incidentally, I was unfamiliar with Chaudhury's extragenomic hypothesis. This sounds even more likely than hypermutation in this case. However, one point which could bear some stressing is the fact that hypermutation occurs within ourselves with the B cells of the adaptive immune system, so it isn't simply isolated to bacteria. However, at this point I doubt that it is of much significance in the evolution of multicellular organisms though it is something to keep in mind: with somatic cells, such as the B cells, it makes sense to experiment with hypermutation since there are so many of them -- much like the progeny of bacteria. Gametes are quite a different story, usually.This message has been edited by TimChase, 12-09-2005 11:29 AM

The study of endogenous retroviruses is becoming a powerful tool in evolutionary science. Moreover, they appear to play an important role in evolution itself -- which is strongly suggested by the fact that approximately half of the human genome is composed of retroelements:"Five retroelement families, L1 and L2 (long interspersed nuclear element, LINE), Alu and MIR (short interspersed nuclear element, SINE), and LTR (long terminal repeat), comprise almost half of the human genome....," fromPeriodic Explosive Expansion of Human retroelements Associated with the Evolution of the Hominoid Primate Tae-Min Kim, Seung-Jin Hong, Mun-Gan Rhyu
J Korean Med Sci 2004; 19: 177-85
http://jkms.kams.or.kr/2004/pdf/04177.pdfYou may also find this interesting: it appears that placental embryos owe their survival to endogenous retroviruses which become active create a barrier to the mother's immune system. Moreover, some of these viruses become expressed during normal embryonic tissue development in a number of organs. In the case of humans, typically three different species of retroviruses are involved in complementary aspects of the creation of this barrier. Moreover, with 30,000 retroviruses per haploid genome (containing perhaps more DNA than in all of our genes combined -- I have seen figures ranging from 1% to 7%, where genes comprise only 1.5%), it would seem likely that other endogenous retroviruses have assumed additional positive, symbiotic functions in relation to their hosts.See:Human Endogenous Retroviruses in Health and Disease: A symbiotic perspective (technical)
by Frank Ryan
Journal of the Royal Society of Medicine
Volume 97 December 2004
http://www.rsm.ac.uk/new/pdfs/j_art_dec04.pdf

May I ask what this entire sequence of posts on mutation and retroviruses etc. has to do with the phylogeographic challenge to creationism which was Mick's OP?

(emphasis added)Sorry, Faith. We were talking about retroviral insertions since they are one form of mutation -- and apparently people got interested in the topic as a matter of friendly chit-chat. It sometimes happens.However, even this has some relevance to phylogeographics -- as some endogenous retroviruses belong to some members of our species, not others. For example, Message 258Seems somewhat relevant to phylogeographics, doesn't it? As a creationist, do you find it at all challenging?This message has been edited by TimChase, 12-10-2005 12:01 AM

For the record, I use copy errors to mean error in the reproduction of the DNA during the reproduction process, whether it adds or deletes segments or places then in the wrong order or direction.

Pehaps a little overstated: this is only copy errors by my definitions, and does not include changes that have occurred in the parent DNA since it's inception ...

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RebelAAmerican.Zen[Deist
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To be honest this doesn't really clarify things. This definition would also include the vast majority of single site mutations which you were defining as distinct from 'copy errors'.By 'reproduction process' do you mean DNA synthesis in general, as in the S phase of the cell cycle, or specifically DNA synthesis ocurring in the gametes?You seem to be making a fairly arbitrary distinction here.TTFN,WK

from wikipedia: This random sampling error would include both your tree falling by a totally random process on an unfortunate victim and the random ommission of one parents genes in the reproduction process, more likely the fewer offspring the parent has.ie -- not all the genes that are lost from one generation to the next are due to selection factors, and those that are due to random factors are lumped together into genetic drift.

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RebelAAmerican.Zen[Deist
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It does include most somatic mutations when you consider a daughter cell to be "offspring" of a parent cell (within the same organism); but to be clear I was specifically referring to mutation in the sense of heredity.In any case, you seemed to be using "mutation" to specifically refer to single nucleotide changes/indels, which is incorrect terminology. You seemed to originally be using "copy errors" (incorrectly) to designate "duplications" - These seemingly incorrect terms were the ones I wanted to clarify in my post; if this isn't how you were intending to use them, then it was a matter of miscommunication.Really, a mutation is any change in the genome, no? From a single nucleotide change to whole genome duplication, it's all mutation.

Which should include all the changes in the DNA accumulated by the parent up to the moment of reproduction - the mutations in it's DNA that have occurred over time since it's {birth\inception}. You seemed to have only included changes during reproduction, hence the comment about overstatement.I chose to distinguish between source changes (reflected in all offspring that get the gene (allowing for sex randomness)) and copy changes (reflected in single offspring). Calling it all mutation to me muddies the waters and is an unnecessary if not counterproductive oversimplification. For any error in making a copy of the DNA during the process of reproduction. Whether duplication, deletion, inversion or whatever.Duplication of course gives the possibility of future change to one copy while leaving the other for its original purpose.

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RebelAAmerican.Zen[Deist
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In one case you have mutations - changes - happening to DNA in a random process independent of reproduction. Radiation whatever.In the other case you have mistakes made in the replication of the DNA.How is this difference arbitrary?

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RebelAAmerican.Zen[Deist
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Now that is you overstating the case quite a bit. The only mutations that the offspring of sexual reproduction will receive are those that end up in the haploid genome of the sperm/egg cell that intiates that offspring (for example mutations in the development/maintenance of the germ line). Definitely not all of the mutations that the parent itself accumulates from inception - quite the opposite - an extremely small number of the parent's total mutations will be passed on to its offspring. But it is all mutation, and it seems that your arbitrary use of terms and distinctions is what is muddying the waters.After all, both "source changes" and "copy changes" are the result of "copy errors" using your definitions. (Talk about confusing things unnecessarily...)Is your own invented terminology or are you getting it from some other source? I sure as hell have never heard these terms before.

I don't know if arbitrary, but it seems incorrect?Both radiation and replication error are sources of mutation in both somatic and germ cells, so your splitting sources of mutation by "independency of reproduction" does not seem valid.Or do you mean single cell "reproduction" exclusively?

I hope no one minds, but since I am somewhat skeptical of the traditional distinction between mutation and heredity, perhaps I could give this a try.I personally don't see a problem with making a distinction between "copy errors" and the "results of random processes" -- that is, if one has a reason for doing so -- a context that requires it. But in much the same way, one could create equally valid distinctions, such as between "retroviral insertions" vs. "mutations which are not the result of retroviral insertions" -- which would include the results of such random processes as the introduction of noise into the copying process. Or likewise, one could distinguish between mutations which are the result of duplications, insertions, deletions, single nucleic polymorphisms, segmental duplications, chromosomal duplications, or triploidy (as distinguished from other forms of polyploidy), and say that that any one of these attributes is the basis for one basic category of mutation, and all other mutations fall into the not-that-category category.But what then is one's basis for selecting on attribute over all others? Well, there is the distinction, such as between copy errors and random processes, but copy errors are themselves the result of a random process -- the introduction of noise into the copying process. Is radiation really any more random than copy errors? What of retroviral insertions? There really isn't any one attribute which stands out above all others -- except possibly in certain contexts.For example, if you wanted to study gene transfer, it might make sense to distinguish between those mutations which are the result of lateral gene transfer (since heredity handles the vertical gene transfer) and those which are not the result of gene transfer. But this would already be imposing an additional context, an additional set of interests or focus, if you will, upon what is essentially a fairly elegant framework -- a framework for studying the effects of heredity (via Mendel). There are those changes in the genetic material which simply due to the normal process of heredity -- then there is everything else.Similarly, if one is interested specifically in the fidelity of the copying process, perhaps the division which you suggest would be attractive. But would it be all that different from a classification based upon a single nucleic polymorphism? Perhaps, but I honestly don't know. Would it be any different from a purely genetic perspective from an "error" due to radiation? In most cases, probably not. Who would it be of interest to? Those who specialize in the study of the fidelity of the copying process -- as opposed to, for example, mitosis or meiosis, either of which might include something as exotic as polyploidy.Whatever additional focus you impose would be of interest to some, but of no interest to a great many others. For example, lateral gene transfer would sometimes be of interest to retrovirologists -- but it wouldn't necessarily be quite the distinction which they would like to make -- since lateral gene transfer doesn't necessarily involve a retrovirus, but may simply take place within the same genome as the result of retrotransposons which were already there.Besides, why would one be particularly interested in lateral gene transfer -- since it isn't that common -- except when it is between bacteria, involves a virus or retrotransposons? Or why, for example, would someone who is studying bacteria wish to put a spotlight on retroviruses? Alternatively, one might choose to focus on those processes which reduce (or alternatively, increase) the size of the genome. (Actually, I can see how Dembski might take an interest in those which increase the size of the genome. I suppose he might call them "acts of intelligence" even though they tend to increase the entropy of the genome -- or perhaps he would actually reserve the term for those which do result in an increase in the entropy. I believe the latter is actually closer to his views.) But such a category would only be so much additional clutter for other uses.(NOTE: I am not sure that I have done justice to either participant's perspective, but I hope that I have not committed any major injustice, either.)This message has been edited by TimChase, 12-09-2005 11:08 PM